Variant report

Variant	rs362296
Chromosome Location	chr4:3247007-3247008
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr4:3246802-3247203	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:3245779-3248772	GM19193	blood:	n/a	n/a
3	BCL3	chr4:3246538-3247516	GM12878	blood:	n/a	chr4:3247225-3247234
4	POLR2A	chr4:3244932-3247517	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:3245637-3248092	GM12892	blood:	n/a	n/a
6	POLR2A	chr4:3246442-3247751	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:3244619-3248406	GM12891	blood:	n/a	n/a
8	POLR2A	chr4:3244931-3248642	GM18505	blood:	n/a	n/a
9	POLR2A	chr4:3246826-3247493	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr4:3244102-3248493	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:3246901-3247143	HepG2	liver:	n/a	n/a
12	POLR2A	chr4:3246040-3247114	HepG2	liver:	n/a	n/a
13	POLR2A	chr4:3245513-3247771	GM15510	blood:	n/a	n/a
14	POLR2A	chr4:3246726-3247099	H1-hESC	embryonic stem cell:	n/a	n/a
15	MTA3	chr4:3245374-3247599	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:3246780-3247635	MCF-7	breast:	n/a	n/a
17	CREB1	chr4:3246926-3247149	A549	lung:	n/a	n/a
18	POLR2A	chr4:3246942-3247525	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr4:3245597-3247902	GM12891	blood:	n/a	n/a
20	POLR2A	chr4:3245740-3247727	GM18951	blood:	n/a	n/a
21	POLR2A	chr4:3244712-3247939	GM12892	blood:	n/a	n/a
22	POLR2A	chr4:3245953-3247652	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr4:3244651-3247810	GM12891	blood:	n/a	n/a
24	POLR2A	chr4:3246753-3247821	GM12878	blood:	n/a	n/a
25	POLR2A	chr4:3245653-3248647	GM12891	blood:	n/a	n/a
26	POLR2A	chr4:3246598-3247316	GM12892	blood:	n/a	n/a
27	POLR2A	chr4:3246611-3247847	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:3245039-3247602	K562	blood:	n/a	n/a
29	ELF1	chr4:3246977-3247282	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:3246795-3247052	GM12891	blood:	n/a	n/a
31	POLR2A	chr4:3244754-3248080	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3243758..3245995-chr4:3246893..3248968,3	K562	blood:
2	chr4:3075638..3077191-chr4:3246487..3249347,2	MCF-7	breast:

Variant related genes	Relation type
MSANTD1	TF binding region
ENSG00000197386	Chromatin interaction
ENSG00000251075	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs108850	0.95[JPT][hapmap]
rs110501	0.84[JPT][hapmap]
rs1547410	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071671	0.89[JPT][hapmap]
rs2071703	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2071704	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2237007	0.83[ASN][1000 genomes]
rs2269478	0.84[ASN][1000 genomes]
rs2269499	0.90[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2798221	0.85[JPT][hapmap]
rs3095075	0.80[ASN][1000 genomes]
rs3095077	0.85[JPT][hapmap]
rs3095081	0.95[JPT][hapmap]
rs3121417	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3121418	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3121419	0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3129322	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3135175	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34155847	0.82[ASN][1000 genomes]
rs362268	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs362271	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs362272	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs362273	0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs362306	0.85[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs362309	0.87[ASN][1000 genomes]
rs362312	0.81[ASN][1000 genomes]
rs362331	0.84[JPT][hapmap]
rs363064	0.85[JPT][hapmap]
rs363096	0.84[JPT][hapmap]
rs3775061	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4690073	0.84[JPT][hapmap]
rs6844859	0.85[JPT][hapmap]
rs7685686	0.85[JPT][hapmap]
rs82333	0.84[JPT][hapmap]
rs916171	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv524211	chr4:3215835-3270488	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv878457	chr4:3231661-3278517	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs362296	MSANTD1	cis	Thyroid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3213800-3247600	Strong transcription	Primary T cells from cord blood	blood
3	chr4:3223400-3247600	Strong transcription	Fetal Brain Female	brain
4	chr4:3231400-3247400	Strong transcription	Spleen	Spleen
5	chr4:3236000-3247400	Strong transcription	Brain Hippocampus Middle	brain
6	chr4:3238000-3259200	Weak transcription	HSMMtube	muscle
7	chr4:3238200-3250200	Weak transcription	Fetal Brain Male	brain
8	chr4:3238200-3255200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:3238200-3261400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:3238600-3259800	Weak transcription	NH-A	brain
11	chr4:3239800-3247600	Genic enhancers	Fetal Stomach	stomach
12	chr4:3241600-3259200	Weak transcription	Small Intestine	intestine
13	chr4:3242200-3248800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:3242200-3252000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:3243000-3247800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:3243000-3260000	Weak transcription	Brain Angular Gyrus	brain
17	chr4:3243200-3251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:3243400-3247400	Weak transcription	Dnd41	blood
19	chr4:3243400-3247600	Weak transcription	Osteobl	bone
20	chr4:3243400-3248600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr4:3243400-3250400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:3243400-3252000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:3243400-3254400	Weak transcription	GM12878-XiMat	blood
24	chr4:3243400-3259200	Weak transcription	Colonic Mucosa	Colon
25	chr4:3243400-3259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:3243600-3247800	Weak transcription	Brain Substantia Nigra	brain
27	chr4:3243600-3258800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr4:3243800-3257400	Weak transcription	Gastric	stomach
29	chr4:3243800-3258000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:3244000-3248400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:3244000-3252200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:3244000-3252200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:3244200-3248200	Weak transcription	HepG2	liver
34	chr4:3244200-3252400	Weak transcription	Fetal Intestine Large	intestine
35	chr4:3244200-3259400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:3244400-3252000	Weak transcription	Fetal Lung	lung
37	chr4:3244600-3248200	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:3244800-3250000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:3244800-3251200	Weak transcription	Brain Anterior Caudate	brain
40	chr4:3244800-3259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:3245000-3247600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:3245000-3255400	Weak transcription	Esophagus	oesophagus
43	chr4:3245200-3247400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr4:3245200-3247600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:3245200-3247800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr4:3245200-3248000	Weak transcription	Placenta	Placenta
47	chr4:3245200-3248200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:3245200-3251800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr4:3245200-3255000	Weak transcription	Pancreas	Pancrea
50	chr4:3245200-3259800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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